Normally, by pressing 2nd ENTER repeatedly, you can cycle through some of the recent entries on the home screen. With the Clear Entries command, this history is cleared (only Clear Entries remains in the history).

This can be used to free some memory, although it's recommended not to do this in a program (because clearing things without asking first isn't nice). Aside from that, maybe the only reason to use Clear Entries is to protect your privacy — although someone looking at your entries will know you cleared something, so it's not that effective.